Insight into the generation of near infra-red (NIR) absorbing species in electrochromic surface-anchored metal-organic frameworks.

Due to their versatility and easy processing, Surface-Anchored Metal-Organic Frameworks (SurMOFs) have gained interest in recent times as promising electrochromic thin films. Herein a step forward in their use and characterization was achieved thanks to the integration of {Zn2(PDICl4)2} SurMOFs in a multi-layer electrochromic device (ECD), based on a membrane-like electrolyte. The optical and electrochemical properties of the ECD were fully characterized, revealing a two-step reduction process localized on the organic ligand and involving subsequent near infra-red (NIR) and cyan absorbing states, leading to optical modulation of the films. The species responsible for this absorption were isolated and identified in the reduced states. In parallel to experimental characterization, quantum chemistry was successfully used to investigate the structure-property relationship of the SurMOF, revealing additional information regarding the structure and the local environment of the electrochromic ligand.

Notes on density matrix perturbation theory.

Density matrix perturbation theory (DMPT) is known as a promising alternative to the Rayleigh-Schrödinger perturbation theory, in which the sum-over-states (SOS) is replaced by algorithms with perturbed density matrices as the input variables. In this article, we formulate and discuss three types of DMPT, with two of them based only on density matrices: the approach of Kussmann and Ochsenfeld [J. Chem. Phys. 127, 054103 (2007)] is reformulated via the Sylvester equation and the recursive DMPT of Niklasson and Challacombe [Phys. Rev. Lett. 92, 193001 (2004)] is extended to the hole-particle canonical purification (HPCP) from Truflandier et al. [J. Chem. Phys. 144, 091102 (2016)]. A comparison of the computational performances shows that the aforementioned methods outperform the standard SOS. The HPCP-DMPT demonstrates stable convergence profiles but at a higher computational cost when compared to the original recursive polynomial method.

Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs.

Aquation free energy profiles of neutral cisplatin and cationic monofunctional derivatives, including triaminochloroplatinum(II) and cis-diammine(pyridine)chloroplatinum(II), were computed using state of the art thermodynamic integration, for which temperature and solvent were accounted for explicitly using density functional theory-based canonical molecular dynamics (DFT-MD). For all the systems, the "inverse-hydration" where the metal center acts as an acceptor of hydrogen bond has been observed. This has motivated to consider the inversely bonded solvent molecule in the definition of the reaction coordinate required to initiate the constrained DFT-MD trajectories. We found that there exists little difference in free enthalpies of activation, such that these platinum-based anticancer drugs are likely to behave the same way in aqueous media. Detailed analysis of the microsolvation structure of the square-planar complexes, along with the key steps of the aquation mechanism, is discussed.

Large scale and linear scaling DFT with the CONQUEST code.

We survey the underlying theory behind the large-scale and linear scaling density functional theory code, conquest, which shows excellent parallel scaling and can be applied to thousands of atoms with diagonalization and millions of atoms with linear scaling. We give details of the representation of the density matrix and the approach to finding the electronic ground state and discuss the implementation of molecular dynamics with linear scaling. We give an overview of the performance of the code, focusing in particular on the parallel scaling, and provide examples of recent developments and applications.

Quadrupolar NMR Relaxation from ab Initio Molecular Dynamics: Improved Sampling and Cluster Models versus Periodic Calculations.

Quadrupolar NMR relaxation rates are computed for 17O and 2H nuclei of liquid water, and of 23Na+, and 35Cl- in aqueous solution via Kohn-Sham (KS) density functional theory ab initio molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of 2 of experimental results and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling. The latter is found to be the more limiting factor in obtaining good statistical sampling and is improved by averaging over many equivalent nuclei of a system or over several independent trajectories. Further, full periodic plane-wave basis calculations of the EFGs are compared with molecular-cluster atomic-orbital basis calculations. The two methods deliver comparable results with nonhybrid functionals. With the molecular-cluster approach, a larger variety of electronic structure methods is available. For chloride, the EFG computations benefit from using a hybrid KS functional.

Uranyl Carbonate Complexes in Aqueous Solution and Their Ligand NMR Chemical Shifts and 17O Quadrupolar Relaxation Studied by ab Initio Molecular Dynamics.

Dynamic structural effects, NMR ligand chemical shifts, and 17O NMR quadrupolar relaxation rates are investigated in the series of complexes UO22+, UO2(CO3)34-, and (UO2)3(CO3)66-. Car-Parrinello molecular dynamics (CPMD) is used to simulate the dynamics of the complexes in water. NMR properties are computed on clusters extracted from the CPMD trajectories. In the UO22+ complex, coordination at the uranium center by water molecules causes a decrease of around 300 ppm for the uranyl 17O chemical shift. The final value of this chemical shift is within 40 ppm of the experimental range. The UO2(CO3)34- and (UO2)3(CO3)66- complexes show a solvent dependence of the terminal carbonate 17O and 13C chemical shifts that is less pronounced than that for the uranyl oxygen atom. Corrections to the chemical shift from hybrid functionals and spin-orbit coupling improve the accuracy of chemical shifts if the sensitivity of the uranyl chemical shift to the uranyl bond length (estimated at 140 ppm per 0.1 Å from trajectory data) is taken into consideration. The experimentally reported trend in the two unique 13C chemical shifts is correctly reproduced for (UO2)3(CO3)66-. NMR relaxation rate data support large 17O peak widths, but remain below those noted in the experimental literature. Comparison of relaxation data for solvent-including versus solvent-free models suggest that carbonate ligand motion overshadows explicit solvent effects.

From cellulose to kerogen: molecular simulation of a geological process.

The process by which organic matter decomposes deep underground to form petroleum and its underlying kerogen matrix has so far remained a no man's land to theoreticians, largely because of the geological (Myears) timescale associated with the process. Using reactive molecular dynamics and an accelerated simulation framework, the replica exchange molecular dynamics method, we simulate the full transformation of cellulose into kerogen and its associated fluid phase under prevailing geological conditions. We observe in sequence the fragmentation of the cellulose crystal and production of water, the development of an unsaturated aliphatic macromolecular phase and its aromatization. The composition of the solid residue along the maturation pathway strictly follows what is observed for natural type III kerogen and for artificially matured samples under confined conditions. After expulsion of the fluid phase, the obtained microporous kerogen possesses the structure, texture, density, porosity and stiffness observed for mature type III kerogen and a microporous carbon obtained by saccharose pyrolysis at low temperature. As expected for this variety of precursor, the main resulting hydrocarbon is methane. The present work thus demonstrates that molecular simulations can now be used to assess, almost quantitatively, such complex chemical processes as petrogenesis in fossil reservoirs and, more generally, the possible conversion of any natural product into bio-sourced materials and/or fuel.

Communication: Generalized canonical purification for density matrix minimization.

A Lagrangian formulation for the constrained search for the N-representable one-particle density matrix based on the McWeeny idempotency error minimization is proposed, which converges systematically to the ground state. A closed form of the canonical purification is derived for which no a posteriori adjustment on the trace of the density matrix is needed. The relationship with comparable methods is discussed, showing their possible generalization through the hole-particle duality. The appealing simplicity of this self-consistent recursion relation along with its low computational complexity could prove useful as an alternative to diagonalization in solving dense and sparse matrix eigenvalue problems.

Quadrupolar NMR Spin Relaxation Calculated Using Ab Initio Molecular Dynamics: Group 1 and Group 17 Ions in Aqueous Solution.

Electric field gradient (EFG) fluctuations for the monoatomic ions (7)Li(+), (23)Na(+), (35)Cl(-), (81)Br(-), and (127)I(-) in aqueous solution are studied using Car-Parrinello ab initio molecular dynamics (aiMD) simulations based on density functional theory. EFG calculations are typically performed with 1024 ion-solvent configurations from the aiMD simulation, using the Zeroth Order Regular Approximation (ZORA) relativistic Hamiltonian. Autocorrelation functions for the spherical EFG tensor elements are computed, transformed into the corresponding spectral densities (under the extreme narrowing condition), and subsequently converted into NMR quadrupolar relaxation rates for the ions. The relaxation rates are compared with experimental data. The order of magnitude is correctly predicted by the simulations. The computational protocol is tested in detail for (81)Br(-).

Atomic contributions from spin-orbit coupling to 29Si NMR chemical shifts in metallasilatrane complexes.

New members of a novel class of metallasilatrane complexes [X-Si-(µ-mt)(4)-M-Y], with M=Ni, Pd, Pt, X=F, Cl, Y=Cl, Br, I, and mt=2-mercapto-1-methylimidazolide, have been synthesized and characterized structurally by X-ray diffraction and by (29)Si solid-state NMR. Spin-orbit (SO) effects on the (29)Si chemical shifts induced by the metal, by the sulfur atoms in the ligand, and by heavy halide ligands Y=Cl, Br, I were investigated with the help of relativistic density functional calculations. Operators used in the calculations were constructed such that SO coupling can selectively be switched off for certain atoms. The unexpectedly large SO effects on the (29)Si shielding in the Ni complex with X=Y=Cl reported recently originate directly from the Ni atom, not from other moderately heavy atoms in the complex. With respect to Pd, SO effects are amplified for Ni owing to its smaller ligand-field splitting, despite the smaller nuclear charge. In the X=Cl, Y=Cl, Br, I series of complexes the Y ligand strongly modulates the (29)Si shift by amplifying or suppressing the metal SO effects. The pronounced delocalization of the partially covalent M←Y bond plays an important role in modulating the (29)Si shielding. We also demonstrate an influence from the X ligand on the (29)Si SO shielding contributions originating at Y. The NMR spectra for [X-Si-(µ-mt)(4)-M-Y] must be interpreted mainly based on electronic and relativistic effects, rather than structural differences between the complexes. The results highlight the sometimes unintuitive role of SO coupling in NMR spectra of complexes containing heavy atoms.

NMR J-coupling constants in cisplatin derivatives studied by molecular dynamics and relativistic DFT.

Solvent effects on J((195)Pt-(15)N) one-bond nuclear spin-spin coupling constants (J(PtN)) of cisplatin [cis-diamminedichloroplatinum(II)] and three cisplatin derivatives are investigated using a combination of density functional theory (DFT) based ab initio molecular dynamics (aiMD) and all-electron relativistic DFT NMR calculations employing the two-component relativistic zeroth-order regular approximation (ZORA). Good agreement with experiment is obtained when explicit solvent molecules are considered and when the computations are performed with a hybrid functional. Spin-orbit coupling causes only small effects on J(PtN) . Key factors contributing to the magnitude of coupling constants are elucidated, with the most significant being the presence of solvent as well as the quality of the density functional and basis set combination. The solvent effects are of the same magnitude as J(PtN) calculated for gas-phase geometries. However, the trends of J(PtN) among the complexes are already present in the gas phase. Results obtained with a continuum solvent model agree quite well with the aiMD results, provided that the Pt solvent-accessible radius is carefully chosen. The aiMD results support the existence of a partial hydrogen-bond-like inverse-hydration-type interaction affording a weak (1)J(Pt⋅⋅⋅H(w)) coupling between the complexes and the coordinating water molecule.

Solvent effects and dynamic averaging of 195Pt NMR shielding in cisplatin derivatives.

The influences of solvent effects and dynamic averaging on the (195)Pt NMR shielding and chemical shifts of cisplatin and three cisplatin derivatives in aqueous solution were computed using explicit and implicit solvation models. Within the density functional theory framework, these simulations were carried out by combining ab initio molecular dynamics (aiMD) simulations for the phase space sampling with all-electron relativistic NMR shielding tensor calculations using the zeroth-order regular approximation. Structural analyses support the presence of a solvent-assisted "inverse" or "anionic" hydration previously observed in similar square-planar transition-metal complexes. Comparisons with computationally less demanding implicit solvent models show that error cancellation is ubiquitous when dealing with liquid-state NMR simulations. After aiMD averaging, the calculated chemical shifts for the four complexes are in good agreement with experiment, with relative deviations between theory and experiment of about 5% on average (1% of the Pt(II) chemical shift range).

DFT-NMR Investigation and (51)V 3QMAS experiments for probing surface oh ligands and the hydrogen-bond network in a polyoxovanadate cluster: the case of Cs(4)[H(2)V(10)O(28)].4H(2)O.

This work shows that the combination of first-principles calculations and (51)V NMR experiments is a powerful tool to elucidate the location of surface hydroxyl groups and to precisely describe the hydrogen bond network in the complex decavanadate cluster Cs(4)[H(2)V(10)O(28)].4H(2)O, enhancing the strength of NMR crystallography. The detailed characterization of H-bond networks for these kinds of inorganic compounds is of primary importance and should benefit from the DFT-NMR predictions by considering explicitly the periodic boundary conditions. The determination of the Cs(4)[H(2)V(10)O(28)].4H(2)O structure by single-crystal X-ray diffraction was not sufficiently accurate to provide the location of protons. From available diffraction data, five different protonated model structures have been built and optimized using DFT-based methods. The possible interconversion of two decavanadate isomers through a proton exchange is evaluated by calculating the energy barrier and recording variable-temperature (1)H MAS NMR spectra. First-principles calculations of (51)V NMR parameters clearly indicate that these parameters are very sensitive to the local intermolecular hydrogen-bonding interactions. Considering the DFT error limits, the fairly good agreement between calculated and experimental NMR parameters arising from the statistical modeling of the data allows the unambiguous assignment of the five (51)V NMR signals and, thus, the location of OH surface ligands in the decavanadate cluster. In particular, first-principles calculations accurately reproduce the (51)V quadrupolar parameters. These results are fully consistent with (51)V 3QMAS NMR spectra recorded with and without (1)H decoupling. Finally, correlations are established between local octahedral VO(6) deformations and (51)V NMR parameters (C(q) and Deltadelta), which will be useful for the characterization of a wide range of chemical species containing vanadium(V).

Probing the solvent shell with 195Pt chemical shifts: density functional theory molecular dynamics study of Pt(II) and Pt(IV) anionic complexes in aqueous solution.

Ab initio molecular dynamics (aiMD) simulations based on density functional theory (DFT) were performed on a set of five anionic platinum complexes in aqueous solution. (195)Pt nuclear magnetic shielding constants were computed with DFT as averages over the aiMD trajectories, using the two-component relativistic zeroth-order regular approximation (ZORA) in order to treat relativistic effects on the Pt shielding tensors. The chemical shifts obtained from the aiMD averages are in good agreement with experimental data. For Pt(II) and Pt(IV) halide complexes we found an intermediate solvent shell interacting with the complexes that causes pronounced solvent effects on the Pt chemical shifts. For these complexes, the magnitude of solvent effects on the Pt shielding constant can be correlated with the surface charge density. For square-planar Pt complexes the aiMD simulations also clearly demonstrate the influence of closely coordinated non-equatorial water molecules on the Pt chemical shift, relating the structure of the solution around the complex to the solvent effects on the metal NMR chemical shift. For the complex [Pt(CN)(4)](2-), the solvent effects on the Pt shielding constant are surprisingly small.